This project provides an interactive application for viewing, adding, adjusting and deleting breakpoint calls from the Arima SV Pipeline. hiccurate has been specifically designed to improve the efficiency and ergonomics of structural variant curation, and provides a strand-aware crosshair and fast navigation tools for modifying breakpoints and adjusting viewing parameters.
This is currently a work in-progress. This project is currently only designed to work with Hi-C files in .hic format and breakpoints in the hic_breakfinder-style .breaks.bedpe format from the Arima SV Pipeline (v1.3).
A prototype of the application is currently hosted at https://wjmn.github.io/static/docs/hiccurate-prototype.html. An internet connection is needed to load some of the CSS styles, but the app is otherwise completely client-side.
| Key | Action |
|---|---|
| Right click Hi-C map on left | Add breakpoint at cursor with current strandness |
1, 2, 3, 4 |
Change crosshair strandness |
w |
Previous breakpoint |
s |
Next breakpoint |
a |
Delete selected breakpoint |
d |
Toggle check selected breakpoint |
q |
Undo last deletion |
The Arima SV Pipeline is developed by Arima Genomics. Support for the Arima SV Pipeline can be found on their GitHub page; thank you Arima for outstanding support with using the Arima SV Pipeline, and to Jon Belton at Arima for proposing the idea for a tool.
This project is built upon the Hi-C viewer from juicebox.js.
This is currently an internal research tool developed at Snuderl Lab, NYU.